nf-core/atacseq

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ATAC-seq peak-calling and QC analysis pipeline

Stars: 229
Forks: 141
Open beginner issues: 0
Indexed issues: 50
Avg merge: 13h 41m
Merged PRs (30d): 1

Dominant language: Nextflow
License: MIT
Last GitHub push: Jul 25, 2026
Latest indexed: Sep 19, 2026
Contributing guide: Contributing guide
Code of conduct: Code of conduct
Beginner labels: No beginner labels indexed

Beginner friendly Everything

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50 open issues indexed

Optional UMI-aware preprocessing for UMI-ATAC-seq (`--with_umi`) Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 45/100

nf-core/atacseq#456 · Opened Sep 11, 2026
Update nf-core modules to latest, and fix subsequent breaking subworkflow input signatures Open

Difficulty 4/5 3-5 days Newbie friendliness 48/100

nf-core/atacseq#447 · Opened Jun 23, 2026
The Usage section said use tab-delimited file but the samplesheet is actually comma-delimited Open

bug

Difficulty 1/5 Under an hour Newbie friendliness 78/100

nf-core/atacseq#444 · Opened May 31, 2026
Error running with "Error nextflow.config:298:14: Unexpected input" Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 48/100

nf-core/atacseq#442 · 3 comments · Opened May 19, 2026
BWA_MEM silently receives 0 tasks when BWA index is built from FASTA (no pre-built index provided) Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 38/100

nf-core/atacseq#438 · Opened Mar 25, 2026
Docker: deprecate docker.userEmulation and use docker.runOptions; mitigates Trim Galore pipe freeze Open

bug

Difficulty 2/5 1-3 hours Newbie friendliness 55/100

nf-core/atacseq#435 · Opened Feb 27, 2026
Generate complete snapshots for all tests Open

enhancement

nf-core/atacseq#427 · 1 assignee · Opened Oct 24, 2025
limiting to NFR in the dev version Open

Difficulty 4/5 3-5 days Newbie friendliness 30/100

nf-core/atacseq#424 · Opened Jul 29, 2025
Error executing process Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 25/100

nf-core/atacseq#421 · Opened May 21, 2025
several peaks correspond to the same gene Open

Difficulty 5/5 Over a week Newbie friendliness 15/100

nf-core/atacseq#418 · Opened Apr 7, 2025
JSON schema: Atacseq Open

nf-core/atacseq#416 · 1 assignee · Opened Mar 24, 2025
Picard modules fail when all memory used Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 35/100

nf-core/atacseq#415 · Opened Mar 13, 2025
CSI Implementation for Larger Genomes Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nf-core/atacseq#414 · 1 comment · Opened Mar 6, 2025
Number of cores calculation for Trimgalore Open

wontfix

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nf-core/atacseq#413 · 1 comment · Opened Feb 25, 2025
ataqv Open

question

Difficulty 4/5 3-5 days Newbie friendliness 25/100

nf-core/atacseq#411 · 2 comments · Opened Feb 10, 2025
Merged Replicates-Feature counts does not use the merged bams Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 38/100

nf-core/atacseq#410 · Opened Feb 1, 2025
Support for Read Lengths Not in {50, 100, 150, 200} Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nf-core/atacseq#408 · Opened Jan 24, 2025
FastQC uses only 10 cores in a 32 core server Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 30/100

nf-core/atacseq#404 · 2 comments · Opened Jan 15, 2025
Please change default MACS2 peak calling to narrow peak Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 35/100

nf-core/atacseq#403 · 2 comments · Opened Jan 12, 2025
Issue when rerunning the pipeline for MACS2 narrow peak Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 25/100

nf-core/atacseq#402 · 3 comments · Opened Jan 12, 2025
Pipeline fails quietly when input fastqs are not found Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 35/100

nf-core/atacseq#401 · Opened Jan 11, 2025
Allow discontinuing replicate numbers Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nf-core/atacseq#397 · 2 reactions · Opened Dec 19, 2024
Compress deeptools `.tab` files and `.fa` genomes as they occupy a lot of space Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 42/100

nf-core/atacseq#395 · Opened Nov 28, 2024
Improve TRIMGALORE by adding pigz to Singularity container Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 38/100

nf-core/atacseq#394 · 1 comment · Opened Nov 27, 2024
ERROR ~ Error executing process > 'PGSCATALOG_PGSCCALC:PGSCCALC:DOWNLOAD_SCOREFILES terminated with an error exit status (8) Open

Difficulty 4/5 3-5 days Newbie friendliness 20/100

nf-core/atacseq#391 · 1 comment · Opened Nov 19, 2024
Latest version still generated MACS2, not MACS3 Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 25/100

nf-core/atacseq#389 · 1 comment · Opened Nov 2, 2024
Scale bar inconsistency across samples Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 20/100

nf-core/atacseq#388 · Opened Oct 31, 2024
Set chromap to not shift reads by default Open

enhancement

nf-core/atacseq#381 · 1 assignee · Opened Sep 27, 2024
ATAC-seq Spike-in control Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 35/100

nf-core/atacseq#380 · 1 comment · 4 reactions · Opened Sep 23, 2024
[404] Page not found: https://nf-co.re/atacseq/2.1.2/docs/output/ Open

bug

Difficulty 1/5 Under an hour Newbie friendliness 45/100

nf-core/atacseq#417 · Opened Aug 19, 2024
Picard "--TMP_DIR" arguments are hardcoded Open

invalid

Difficulty 2/5 1-3 hours Newbie friendliness 45/100

nf-core/atacseq#378 · 1 comment · Opened Aug 16, 2024
ERROR ~ Error executing process > 'NFCORE_ATACSEQ:ATACSEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 20/100

nf-core/atacseq#377 · 1 comment · 1 reaction · Opened Aug 10, 2024
New release please? Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

nf-core/atacseq#373 · 2 comments · Opened Jul 4, 2024
Feature Request: call peaks for each replicate (diffbind), not only the merged data Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 35/100

nf-core/atacseq#367 · 5 comments · Opened Jun 28, 2024
suggestion: use samtools view --uncompressed before piping in bamtools_filter Open

enhancement

Difficulty 1/5 Under an hour Newbie friendliness 35/100

nf-core/atacseq#346 · Opened Jan 26, 2024
Feature Request: summary table for each sample Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nf-core/atacseq#345 · 1 comment · 1 reaction · Opened Jan 26, 2024
bam_csi_index parameter for ATACSeq Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 45/100

nf-core/atacseq#343 · Opened Dec 20, 2023
implement the bam_csi_index parameter in atacseq pipeline Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 42/100

nf-core/atacseq#340 · Opened Oct 27, 2023
MAKE_GENE_BED making 0kb .bed files Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

nf-core/atacseq#334 · Opened Sep 6, 2023
CSI bam index not working Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 25/100

nf-core/atacseq#327 · 1 comment · Opened Aug 10, 2023
Biotype analysis using featureCounts Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

nf-core/atacseq#188 · Opened Aug 11, 2022
Peak calling parameters might not be ideal Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 30/100

nf-core/atacseq#169 · 3 comments · Opened Feb 17, 2022
Genome annotation (gene names) missing in IGV session file Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 35/100

nf-core/atacseq#168 · 1 comment · Opened Feb 17, 2022
Does nf-core/atacseq apply an offset to each ATAC-seq fragment? Open

question

Difficulty 3/5 1-2 days Newbie friendliness 25/100

nf-core/atacseq#164 · 3 comments · 2 reactions · Opened Sep 22, 2021
Addition of peak-calling with Genrich Open

enhancement

nf-core/atacseq#108 · 2 reactions · 2 assignees · Opened Jun 13, 2020
Adding the feature of shifting and splitting the reads Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 28/100

nf-core/atacseq#91 · 4 comments · 2 reactions · Opened Mar 4, 2020
Implement Hidden-Markow-Models implemented in ChromstaR for genome-wide characterization of open chromatin landscape Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

nf-core/atacseq#89 · Opened Feb 28, 2020
Create md5 sums for data upload to public repositories Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nf-core/atacseq#32 · Opened Apr 13, 2019
Add single-cell analysis functionality Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 20/100

nf-core/atacseq#25 · 1 reaction · Opened Apr 5, 2019
Add IDR analysis Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

nf-core/atacseq#36 · 2 comments · 5 reactions · Opened Feb 12, 2019

nf-core/atacseq

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